+ public void removeAllVAMSAS() {
+ this._VAMSASList.clear();
+ }
+
+ /**
+ * Method removeApplicationData.
+ *
+ * @param vApplicationData
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeApplicationData(
+ final uk.ac.vamsas.objects.core.ApplicationData vApplicationData) {
+ boolean removed = _applicationDataList.remove(vApplicationData);
+ return removed;
+ }
+
+ /**
+ * Method removeApplicationDataAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.ApplicationData removeApplicationDataAt(
+ final int index) {
+ java.lang.Object obj = this._applicationDataList.remove(index);
+ return (uk.ac.vamsas.objects.core.ApplicationData) obj;
+ }
+
+ /**
+ * Method removeAttachment.
+ *
+ * @param vAttachment
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAttachment(
+ final uk.ac.vamsas.objects.core.Attachment vAttachment) {
+ boolean removed = _attachmentList.remove(vAttachment);
+ return removed;
+ }
+
+ /**
+ * Method removeAttachmentAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Attachment removeAttachmentAt(final int index) {
+ java.lang.Object obj = this._attachmentList.remove(index);
+ return (uk.ac.vamsas.objects.core.Attachment) obj;
+ }
+
+ /**
+ * Method removeVAMSAS.
+ *
+ * @param vVAMSAS
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeVAMSAS(final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS) {
+ boolean removed = _VAMSASList.remove(vVAMSAS);
+ return removed;
+ }
+
+ /**
+ * Method removeVAMSASAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.VAMSAS removeVAMSASAt(final int index) {
+ java.lang.Object obj = this._VAMSASList.remove(index);
+ return (uk.ac.vamsas.objects.core.VAMSAS) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vApplicationData
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setApplicationData(final int index,
+ final uk.ac.vamsas.objects.core.ApplicationData vApplicationData)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._applicationDataList.size()) {
+ throw new IndexOutOfBoundsException("setApplicationData: Index value '"
+ + index + "' not in range [0.."
+ + (this._applicationDataList.size() - 1) + "]");
+ }
+
+ this._applicationDataList.set(index, vApplicationData);
+ }
+
+ /**
+ *
+ *
+ * @param vApplicationDataArray
+ */
+ public void setApplicationData(
+ final uk.ac.vamsas.objects.core.ApplicationData[] vApplicationDataArray) {
+ // -- copy array
+ _applicationDataList.clear();
+
+ for (int i = 0; i < vApplicationDataArray.length; i++) {
+ this._applicationDataList.add(vApplicationDataArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_applicationDataList' by copying the given Vector. All
+ * elements will be checked for type safety.
+ *
+ * @param vApplicationDataList
+ * the Vector to copy.
+ */
+ public void setApplicationData(final java.util.Vector vApplicationDataList) {
+ // copy vector
+ this._applicationDataList.clear();
+
+ this._applicationDataList.addAll(vApplicationDataList);
+ }
+
+ /**
+ * Sets the value of '_applicationDataList' by setting it to the given Vector.
+ * No type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param applicationDataVector
+ * the Vector to set.
+ */
+ public void setApplicationDataAsReference(
+ final java.util.Vector applicationDataVector) {
+ this._applicationDataList = applicationDataVector;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAttachment
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAttachment(final int index,
+ final uk.ac.vamsas.objects.core.Attachment vAttachment)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._attachmentList.size()) {
+ throw new IndexOutOfBoundsException("setAttachment: Index value '"
+ + index + "' not in range [0.." + (this._attachmentList.size() - 1)
+ + "]");
+ }
+
+ this._attachmentList.set(index, vAttachment);
+ }
+
+ /**
+ *
+ *
+ * @param vAttachmentArray
+ */
+ public void setAttachment(
+ final uk.ac.vamsas.objects.core.Attachment[] vAttachmentArray) {
+ // -- copy array
+ _attachmentList.clear();
+
+ for (int i = 0; i < vAttachmentArray.length; i++) {
+ this._attachmentList.add(vAttachmentArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_attachmentList' by copying the given Vector. All
+ * elements will be checked for type safety.
+ *
+ * @param vAttachmentList
+ * the Vector to copy.
+ */
+ public void setAttachment(final java.util.Vector vAttachmentList) {
+ // copy vector
+ this._attachmentList.clear();
+
+ this._attachmentList.addAll(vAttachmentList);
+ }
+
+ /**
+ * Sets the value of '_attachmentList' by setting it to the given Vector. No
+ * type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param attachmentVector
+ * the Vector to set.
+ */
+ public void setAttachmentAsReference(final java.util.Vector attachmentVector) {
+ this._attachmentList = attachmentVector;
+ }
+
+ /**
+ * Sets the value of field 'lockFile'.
+ *
+ * @param lockFile
+ * the value of field 'lockFile'.
+ */
+ public void setLockFile(final uk.ac.vamsas.objects.core.LockFile lockFile) {
+ this._lockFile = lockFile;
+ }
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance
+ * the value of field 'provenance'.
+ */
+ public void setProvenance(
+ final uk.ac.vamsas.objects.core.Provenance provenance) {
+ this._provenance = provenance;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vVAMSAS
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setVAMSAS(final int index,
+ final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._VAMSASList.size()) {
+ throw new IndexOutOfBoundsException("setVAMSAS: Index value '" + index
+ + "' not in range [0.." + (this._VAMSASList.size() - 1) + "]");
+ }
+
+ this._VAMSASList.set(index, vVAMSAS);
+ }
+
+ /**
+ *
+ *
+ * @param vVAMSASArray
+ */
+ public void setVAMSAS(final uk.ac.vamsas.objects.core.VAMSAS[] vVAMSASArray) {
+ // -- copy array
+ _VAMSASList.clear();
+
+ for (int i = 0; i < vVAMSASArray.length; i++) {
+ this._VAMSASList.add(vVAMSASArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_VAMSASList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vVAMSASList
+ * the Vector to copy.
+ */
+ public void setVAMSAS(final java.util.Vector vVAMSASList) {
+ // copy vector
+ this._VAMSASList.clear();
+
+ this._VAMSASList.addAll(vVAMSASList);
+ }
+
+ /**
+ * Sets the value of '_VAMSASList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param VAMSASVector
+ * the Vector to set.
+ */
+ public void setVAMSASAsReference(final java.util.Vector VAMSASVector) {
+ this._VAMSASList = VAMSASVector;
+ }
+
+ /**
+ * Sets the value of field 'version'. The field 'version' has the following
+ * description: Vamsas Document Version Number
+ *
+ * @param version
+ * the value of field 'version'.
+ */
+ public void setVersion(final java.lang.String version) {
+ this._version = version;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled uk.ac.vamsas.objects.core.VamsasDocument
+ */
+ public static uk.ac.vamsas.objects.core.VamsasDocument unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.VamsasDocument) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.VamsasDocument.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }